Mime Jr.'s not as far out as you might think. It does still match up with Mr. Mime. Think about it - if you have Mr. John Smith, and he has a kid he names John, is the son named Jr. John Smith? No. He's John Smith Jr.
Besides, every generation has bad/unimaginative names. Take, for example, Manectric. I personally don't mind it, but it's gotten a lot of flak for being unimaginative, horrible compared to its perfectly good romanization, and so on. Yet Gen. 3 had good names, as you pointed out. Also, Gen. 4 has clever names anyway - take Bonsly. It's a fairly clever, in my opinion, pun.
Long story short, I believe you're overreacting.